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- PDB-9rpk: Apo structure of Arabidopsis thaliana nicotinate mononucleotide a... -

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Basic information

Entry
Database: PDB / ID: 9rpk
TitleApo structure of Arabidopsis thaliana nicotinate mononucleotide adenylyltransferase
ComponentsNicotinamide/nicotinic acid mononucleotide adenylyltransferase
KeywordsTRANSFERASE / NAD metabolism / NaMN / Arabidopsis thaliana / NaMNAT
Function / homology
Function and homology information


nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD+ biosynthetic process / ATP binding / metal ion binding / nucleus
Similarity search - Function
Nicotinamide/nicotinate mononucleotide adenylyltransferase, eukaryotic / : / Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Nicotinamide/nicotinic acid mononucleotide adenylyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSorci, L. / Cianci, M. / Fortunato, C. / Gasparrini, M. / Raffaelli, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Arabidopsis thaliana nicotinate mononucleotide adenylyltransferase: unveiling the molecular determinants and evolutionary origin of nicotinic acid mononucleotide recognition.
Authors: Sorci, L. / Cianci, M. / Fortunato, C. / Gasparrini, M. / Raffaelli, N.
History
DepositionJun 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotinamide/nicotinic acid mononucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8605
Polymers29,7681
Non-polymers924
Water93752
1
A: Nicotinamide/nicotinic acid mononucleotide adenylyltransferase
hetero molecules

A: Nicotinamide/nicotinic acid mononucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,72010
Polymers59,5362
Non-polymers1848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2900 Å2
ΔGint-58 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.563, 43.563, 435.017
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-451-

HOH

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Components

#1: Protein Nicotinamide/nicotinic acid mononucleotide adenylyltransferase / NMN/NaMN adenylyltransferase / Nicotinamide mononucleotide adenylyltransferase / NMN ...NMN/NaMN adenylyltransferase / Nicotinamide mononucleotide adenylyltransferase / NMN adenylyltransferase / Nicotinate-nucleotide adenylyltransferase / NaMN adenylyltransferase


Mass: 29768.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NMNAT, At5g55810, MDF20.25 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: F4K687, nicotinamide-nucleotide adenylyltransferase, nicotinate-nucleotide adenylyltransferase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM TRIS pH 8-9, 100-200 mM MgCl2, and 20-40% (w/v) poly ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.15→37.73 Å / Num. obs: 14722 / % possible obs: 99.84 % / Observed criterion σ(I): 2 / Redundancy: 20 % / Biso Wilson estimate: 41.58 Å2 / CC1/2: 0.996 / CC star: 1 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.042 / Net I/σ(I): 9.6
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 14322 / CC1/2: 0.889 / CC star: 0.99 / Rpim(I) all: 0.218 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MOSFLM7.2.2data reduction
XDSBUILT=20210323data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→37.73 Å / SU ML: 0.1841 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 24.2827
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2563 732 4.98 %
Rwork0.2328 13969 -
obs0.234 14701 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.91 Å2
Refinement stepCycle: LAST / Resolution: 2.15→37.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 4 52 1834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241816
X-RAY DIFFRACTIONf_angle_d0.5412455
X-RAY DIFFRACTIONf_chiral_restr0.0403286
X-RAY DIFFRACTIONf_plane_restr0.0064311
X-RAY DIFFRACTIONf_dihedral_angle_d22.2869685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.320.28551350.24612666X-RAY DIFFRACTION99.75
2.32-2.550.27331480.25852709X-RAY DIFFRACTION99.83
2.55-2.920.28571560.26892720X-RAY DIFFRACTION99.69
2.92-3.680.3031510.24972784X-RAY DIFFRACTION99.9
3.68-37.730.21781420.213090X-RAY DIFFRACTION99.97

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